Chapter 6 Community composition

load("data/data.Rdata")

6.1 Taxonomy overview

6.1.1 Stacked barplot

genome_counts_filt %>%
  mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
  pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
  left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
  left_join(., sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
  filter(count > 0) %>% #filter 0 counts
  filter(!region %in% c("Eskoriatza","Villabona")) %>% 
  mutate(season=factor(season,levels=c("spring","autumn"))) %>% 
  ggplot(., aes(x=sample,y=count, fill=phylum, group=phylum)) + #grouping enables keeping the same sorting of taxonomic units
    geom_bar(stat="identity", colour="white", linewidth=0.1) + #plot stacked bars with white borders
    scale_fill_manual(values=phylum_colors) +
    facet_nested(. ~ region + season,  scales="free") + #facet per day and treatment
    guides(fill = guide_legend(ncol = 1)) +
    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
          axis.title.x = element_blank(),
          panel.background = element_blank(),
          panel.border = element_blank(),
          panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          axis.line = element_line(linewidth = 0.5, linetype = "solid", colour = "black")) +
   labs(fill="Phylum",y = "Relative abundance",x="Samples")

6.1.2 Phylum relative abundances

phylum_summary <- genome_counts_filt %>%
  mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
  pivot_longer(-genome, names_to = "sample", values_to = "count") %>%
  left_join(sample_metadata, by = join_by(sample == sample)) %>%
  left_join(genome_metadata, by = join_by(genome == genome)) %>%
  group_by(sample,phylum) %>%
  summarise(relabun=sum(count))

phylum_summary %>%
    group_by(phylum) %>%
    summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
    arrange(-mean) %>%
    tt()
tinytable_c68egya5dt87b32yf8v6
phylum mean sd
p__Bacteroidota 5.343095e-01 0.2519907920
p__Pseudomonadota 1.645302e-01 0.2419531297
p__Bacillota_A 1.173726e-01 0.1119657856
p__Verrucomicrobiota 6.425495e-02 0.1307490386
p__Bacillota 3.864721e-02 0.0557437562
p__Desulfobacterota 2.040387e-02 0.0455321718
p__Cyanobacteriota 1.229173e-02 0.0511979549
p__Chloroflexota 9.260914e-03 0.0348103508
p__Bacillota_C 7.321975e-03 0.0141655787
p__Fusobacteriota 5.510315e-03 0.0138032117
p__Acidobacteriota 4.080066e-03 0.0190287052
p__Myxococcota 4.068355e-03 0.0400686546
p__Deferribacterota 3.293351e-03 0.0101979152
p__Halobacteriota 2.359186e-03 0.0198236928
p__Planctomycetota 2.008858e-03 0.0118013745
p__Bacillota_B 1.960581e-03 0.0031366435
p__Patescibacteria 1.911343e-03 0.0075513434
p__Desulfobacterota_F 1.150444e-03 0.0052791223
p__Omnitrophota 9.022635e-04 0.0055473998
p__Spirochaetota 7.487452e-04 0.0040145371
p__Thermoproteota 6.566364e-04 0.0024634359
p__Methanobacteriota 5.711150e-04 0.0038712346
p__Campylobacterota 5.678102e-04 0.0028643134
p__ 4.695129e-04 0.0039676126
p__Fibrobacterota 3.213383e-04 0.0031648149
p__Actinomycetota 3.002860e-04 0.0015353729
p__Nanoarchaeota 2.012785e-04 0.0017966105
p__Desulfobacterota_G 1.890416e-04 0.0015463557
p__J088 1.850776e-04 0.0009813572
p__Chlamydiota 9.517468e-05 0.0004833040
p__JAKLEM01 3.852292e-05 0.0003794068
p__Iainarchaeota 1.778707e-05 0.0001338011
phylum_arrange <- phylum_summary %>%
    group_by(phylum) %>%
    summarise(mean=mean(relabun)) %>%
    arrange(-mean) %>%
    select(phylum) %>%
    pull()

phylum_summary %>%
    filter(phylum %in% phylum_arrange) %>%
    mutate(phylum=factor(phylum,levels=rev(phylum_arrange))) %>%
    ggplot(aes(x=relabun, y=phylum, group=phylum, color=phylum)) +
        scale_color_manual(values=phylum_colors[rev(phylum_arrange)]) +
        geom_jitter(alpha=0.5) + 
        theme_minimal() + 
        theme(legend.position="none") +
        labs(y="Phylum",x="Relative abundance")

6.2 Taxonomy boxplot

6.2.1 Family

family_summary <- genome_counts_filt %>%
  mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
  pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
  left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
  left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
  group_by(sample,family) %>%
  summarise(relabun=sum(count))

family_summary %>%
    group_by(family) %>%
    summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
    arrange(-mean) %>%
    tt()
tinytable_6owp328en39o6hkorigv
family mean sd
f__Bacteroidaceae 2.102427e-01 1.955594e-01
f__Rikenellaceae 1.611894e-01 1.562459e-01
f__Tannerellaceae 7.299129e-02 6.664188e-02
f__Aeromonadaceae 5.225319e-02 1.358185e-01
f__Akkermansiaceae 4.800341e-02 1.226970e-01
f__Marinifilaceae 4.290443e-02 4.962259e-02
f__Lachnospiraceae 3.407472e-02 4.248629e-02
f__Ruminococcaceae 3.081005e-02 2.965309e-02
f__Deianiraeaceae 2.805932e-02 1.434462e-01
f__Mycoplasmoidaceae 2.649540e-02 4.798929e-02
f__Enterobacteriaceae 2.607933e-02 7.653830e-02
f__ 2.249364e-02 2.866260e-02
f__Clostridiaceae 1.941957e-02 4.169059e-02
f__Chromatiaceae 1.597569e-02 6.719385e-02
f__Desulfovibrionaceae 1.448492e-02 1.705853e-02
f__Erysipelotrichaceae 1.104908e-02 1.821438e-02
f__Butyricicoccaceae 9.720683e-03 4.494263e-02
f__Diplorickettsiaceae 8.263333e-03 7.249115e-02
f__Chlorobiaceae 8.082269e-03 5.368685e-02
f__CAIVKH01 6.960373e-03 4.385676e-02
f__Chromobacteriaceae 5.687977e-03 3.831936e-02
f__Fusobacteriaceae 5.510315e-03 1.380321e-02
f__Cellulosilyticaceae 5.241853e-03 9.208240e-03
f__VadinHA17 5.088929e-03 1.977358e-02
f__P3 5.008918e-03 1.069121e-02
f__FACHB-T130 4.282697e-03 4.152157e-02
f__Smithellaceae 4.231674e-03 3.872303e-02
f__Oscillospiraceae 4.122127e-03 4.776696e-03
f__Polyangiaceae 4.068355e-03 4.006865e-02
f__SHND01 4.066311e-03 2.670163e-02
f__CAG-239 3.660798e-03 6.287971e-03
f__Chitinophagaceae 3.547368e-03 1.671262e-02
f__Rhodocyclaceae 3.546631e-03 1.999856e-02
f__Methylomonadaceae 3.358104e-03 2.173751e-02
f__Gastranaerophilaceae 3.310922e-03 6.652166e-03
f__Mucispirillaceae 3.293351e-03 1.019792e-02
f__Microcoleaceae 3.259645e-03 2.029315e-02
f__UBA6186 2.990942e-03 2.556453e-02
f__EnvOPS12 2.866794e-03 9.720216e-03
f__UBA11358 2.831247e-03 1.079693e-02
f__Anaerovoracaceae 2.355592e-03 2.819219e-03
f__UBA1997 2.353806e-03 6.323583e-03
f__Peptostreptococcaceae 2.204895e-03 8.095665e-03
f__Pumilibacteraceae 2.190757e-03 6.124917e-03
f__CHK158-818 2.050734e-03 3.904830e-03
f__Peptococcaceae 1.960581e-03 3.136644e-03
f__Muribaculaceae 1.944857e-03 3.177931e-03
f__Methanotrichaceae 1.861022e-03 1.802606e-02
f__Burkholderiaceae_B 1.860907e-03 8.600392e-03
f__Methylococcaceae 1.799044e-03 1.156777e-02
f__Palsa-965 1.607561e-03 1.047557e-02
f__Competibacteraceae 1.594056e-03 1.515395e-02
f__UBA3637 1.458445e-03 3.362239e-03
f__Prolixibacteraceae 1.429249e-03 6.122270e-03
f__UBA5704 1.424231e-03 1.402705e-02
f__B-1AR 1.402641e-03 1.006339e-02
f__Chloroflexaceae 1.400177e-03 1.355414e-02
f__Succinispiraceae 1.397250e-03 2.545125e-03
f__B-17BO 1.328598e-03 8.384278e-03
f__Microcystaceae_B 1.272683e-03 1.173539e-02
f__FEN-979 1.241677e-03 7.686017e-03
f__Pirellulaceae 1.154158e-03 9.332434e-03
f__Massilibacillaceae 1.109284e-03 5.877503e-03
f__Methylophilaceae 1.037785e-03 5.355410e-03
f__Beijerinckiaceae 1.035186e-03 4.457229e-03
f__CAG-465 9.274101e-04 4.611188e-03
f__Ignavibacteriaceae 9.217538e-04 8.213255e-03
f__Anaerotignaceae 9.086293e-04 1.650081e-03
f__Profunditerraquicolaceae 9.022635e-04 5.547400e-03
f__Pseudopelobacteraceae 8.857441e-04 5.074400e-03
f__UBA4417 8.455976e-04 5.163518e-03
f__UBA5066 8.403140e-04 5.601038e-03
f__UBA3700 8.067207e-04 2.729698e-03
f__Pyrinomonadaceae 7.220263e-04 5.094091e-03
f__Opitutaceae 7.101304e-04 6.993974e-03
f__Victivallaceae 7.026208e-04 3.743327e-03
f__Thermoanaerobaculaceae 6.814796e-04 6.711796e-03
f__HGW-15 6.374558e-04 4.579831e-03
f__4484-276 6.317310e-04 4.568187e-03
f__Acutalibacteraceae 6.098025e-04 4.563323e-03
f__Paludibacteraceae 5.835103e-04 5.070989e-03
f__Methanobacteriaceae 5.711150e-04 3.871235e-03
f__UBA10030 5.519425e-04 3.031739e-03
f__OLB5 5.252756e-04 3.582377e-03
f__UBA3830 5.136412e-04 1.407875e-03
f__F082 4.928572e-04 3.895817e-03
f__Shewanellaceae 4.927823e-04 2.267869e-03
f__DYRC01 4.772738e-04 4.700602e-03
f__Sedimentibacteraceae 4.667661e-04 1.389224e-03
f__JADJPG01 4.263615e-04 2.960895e-03
f__UBA932 4.156228e-04 1.178640e-03
f__Fen-1058 4.086113e-04 3.836266e-03
f__Arcobacteraceae 3.795084e-04 2.546493e-03
f__UBA927 3.720772e-04 1.914678e-03
f__Rectinemataceae 3.564056e-04 3.510188e-03
f__WRBN01 3.333468e-04 1.999495e-03
f__GWF2-50-10 3.327121e-04 2.480457e-03
f__Steroidobacteraceae 3.265626e-04 2.177059e-03
f__Hepatoplasmataceae 2.940398e-04 2.271892e-03
f__Planctomycetaceae 2.891817e-04 2.848110e-03
f__Methanocorpusculaceae 2.866192e-04 1.094065e-03
f__UBA4823 2.816756e-04 2.774183e-03
f__Staskawiczbacteraceae 2.657578e-04 2.400392e-03
f__CAIRTM01 2.647003e-04 1.610403e-03
f__UBA4778 2.605813e-04 1.471595e-03
f__Coprobacillaceae 2.512556e-04 7.367047e-04
f__JAAUTT01 2.497687e-04 1.342951e-03
f__Spirosomaceae 2.470890e-04 1.347542e-03
f__JAAYKM01 2.396380e-04 2.360160e-03
f__UBA3254 2.373440e-04 1.827176e-03
f__Gemmataceae 2.328062e-04 2.292876e-03
f__Saprospiraceae 2.317820e-04 1.292124e-03
f__UBA660 2.309557e-04 1.425198e-03
f__Holophagaceae 2.166536e-04 2.133790e-03
f__UBA12108 2.154250e-04 1.514456e-03
f__2-12-FULL-35-15 2.127537e-04 1.727718e-03
f__Methanoregulaceae 2.115446e-04 1.818352e-03
f__GW2011-AR1 2.012785e-04 1.796610e-03
f__Terrimicrobiaceae 1.978209e-04 7.709831e-04
f__Acidobacteriaceae 1.953616e-04 1.924089e-03
f__Syntrophorhabdaceae 1.890416e-04 1.546356e-03
f__UBA6016 1.883018e-04 1.303750e-03
f__UBA3375 1.862708e-04 7.937741e-04
f__Flavobacteriaceae 1.829016e-04 1.620468e-03
f__DUVY01 1.822525e-04 5.064739e-04
f__SHXO01 1.797211e-04 8.927506e-04
f__RUG14156 1.657852e-04 9.670025e-04
f__UBA2023 1.651542e-04 1.140732e-03
f__SPBP01 1.589463e-04 1.014813e-03
f__LL51 1.572266e-04 9.059455e-04
f__Crocinitomicaceae 1.549871e-04 1.052732e-03
f__2-12-FULL-60-25 1.541342e-04 1.081327e-03
f__Lutisporaceae 1.460459e-04 3.785647e-04
f__Aestuariivirgaceae 1.447142e-04 5.908593e-04
f__Eubacteriaceae 1.393410e-04 4.869468e-04
f__SG8-41 1.297459e-04 9.992533e-04
f__UBA9973 1.294228e-04 9.028722e-04
f__UBA5976 1.252602e-04 7.247546e-04
f__UBA1820 1.181123e-04 2.910814e-04
f__Sphingomonadaceae 1.152657e-04 5.446202e-04
f__Absconditicoccaceae 1.132011e-04 8.067896e-04
f__Ilumatobacteraceae 1.119473e-04 7.628420e-04
f__TH1-2 1.094839e-04 6.706470e-04
f__Rhabdochlamydiaceae 9.517468e-05 4.833040e-04
f__Amoebophilaceae 9.033159e-05 5.611765e-04
f__Mycoplasmataceae 8.841740e-05 5.867263e-04
f__Burkholderiaceae 8.225897e-05 3.422233e-04
f__JAGQMS01 7.555860e-05 3.616569e-04
f__JAFDDL01 7.232997e-05 7.123676e-04
f__Tenuifilaceae 7.192224e-05 5.390355e-04
f__Burkholderiaceae_A 6.890317e-05 6.000937e-04
f__Rhizobiaceae 6.770667e-05 3.322745e-04
f__UBA5272 6.344839e-05 5.321556e-04
f__JAGOQP01 6.336248e-05 6.240480e-04
f__Microbacteriaceae 6.307851e-05 4.535380e-04
f__SZUA-47 6.279603e-05 3.586105e-04
f__Moraxellaceae 5.992173e-05 4.649041e-04
f__Brevinemataceae 5.899281e-05 3.455812e-04
f__CAG-508 5.239573e-05 3.378165e-04
f__UBA1709 5.179159e-05 5.100880e-04
f__UBA1568 4.952088e-05 2.986606e-04
f__XYD1-FULL-46-19 4.915817e-05 4.354164e-04
f__JAKLEM01 3.852292e-05 3.794068e-04
f__CAIOMD01 3.103415e-05 1.937893e-04
f__GWA2-36-10 2.884440e-05 2.345672e-04
f__PALSA-1337 2.249398e-05 1.820714e-04
f__UBA12049 1.906267e-05 1.685139e-04
f__JAAZKV01 1.778707e-05 1.338011e-04
f__Zambryskibacteraceae 1.740558e-05 1.410053e-04
f__UBA920 1.348493e-05 9.984023e-05
family_arrange <- family_summary %>%
    group_by(family) %>%
    summarise(mean=sum(relabun)) %>%
    arrange(-mean) %>%
    select(family) %>%
    pull()

# Per origin
family_summary %>%
    left_join(genome_metadata %>% select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
    left_join(sample_metadata,by=join_by(sample==sample)) %>%
    filter(family %in% family_arrange[1:20]) %>%
    mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
    filter(relabun > 0) %>%
    ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
        scale_color_manual(values=phylum_colors[-8]) +
        geom_jitter(alpha=0.5) + 
        facet_grid(.~region)+
        theme_minimal() + 
        labs(y="Family", x="Relative abundance", color="Phylum")

# Per season
family_summary %>%
    left_join(genome_metadata %>% select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
    left_join(sample_metadata,by=join_by(sample==sample)) %>%
    filter(family %in% family_arrange[1:20]) %>%
    mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
    filter(relabun > 0) %>%
    ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
        scale_color_manual(values=phylum_colors[-8]) +
        geom_jitter(alpha=0.5) + 
        facet_grid(.~season)+
        theme_minimal() + 
        labs(y="Family", x="Relative abundance", color="Phylum")

6.2.2 Genus

genus_summary <- genome_counts_filt %>%
  mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
  pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
  left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
  left_join(genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
  group_by(sample,phylum,genus) %>%
  summarise(relabun=sum(count)) %>%
  filter(genus != "g__") %>%
  mutate(genus= sub("^g__", "", genus))

genus_summary_sort <- genus_summary %>%
    group_by(genus) %>%
    summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
    arrange(-mean) 

genus_summary_sort %>%
    tt()
tinytable_bd153y65zlbpszmi5qc6
genus mean sd
Bacteroides 2.046402e-01 1.953733e-01
Mucinivorans 9.924394e-02 1.365473e-01
Parabacteroides 6.237195e-02 5.788498e-02
Aeromonas 5.225319e-02 1.358185e-01
CAJQOT01 2.805932e-02 1.434462e-01
Odoribacter 2.218113e-02 3.013106e-02
Luteolibacter 2.154040e-02 1.200740e-01
Mycoplasma_L 2.040488e-02 4.176073e-02
Akkermansia 1.792041e-02 3.645298e-02
JADFUS01 1.681497e-02 1.658130e-02
Rikenella 1.564868e-02 2.937705e-02
Clostridium 1.199086e-02 2.212868e-02
Thiodictyon 1.147645e-02 4.824596e-02
Parabacteroides_B 1.010987e-02 1.489169e-02
Hafnia 9.663663e-03 3.830939e-02
UBA866 9.264589e-03 1.479609e-02
Aquirickettsiella 8.263333e-03 7.249115e-02
Sarcina 7.428710e-03 2.241766e-02
CAIVKH01 6.960373e-03 4.385676e-02
SZUA-378 6.661372e-03 1.838064e-02
Buttiauxella 6.566993e-03 2.598993e-02
Malacoplasma 6.090519e-03 2.462978e-02
Chlorobaculum 5.395630e-03 3.800456e-02
LD21 5.088929e-03 1.977358e-02
Citrobacter 4.984853e-03 4.796159e-02
Clostridium_Q 4.898432e-03 5.777642e-03
Alistipes 4.515880e-03 6.268518e-03
Hydrogenoanaerobacterium 4.388173e-03 9.024943e-03
FACHB-831 4.282697e-03 4.152157e-02
Vogesella 4.209095e-03 3.678975e-02
Smithella 4.156714e-03 3.798709e-02
SHND01 4.066311e-03 2.670163e-02
OM05-12 3.832406e-03 7.079937e-03
Angelakisella 3.793239e-03 4.933497e-03
Mobilisporobacter 3.653987e-03 1.032287e-02
Hungatella_A 3.630470e-03 6.092968e-03
RUG14305 3.311659e-03 4.971494e-03
JAGNZR01 3.281321e-03 9.557152e-03
Planktothrix 3.259645e-03 2.029315e-02
Tidjanibacter 3.180993e-03 5.865598e-03
UBA6186 2.990942e-03 2.556453e-02
FEN-1139 2.985961e-03 2.940831e-02
UMGS1251 2.826349e-03 4.504858e-03
UBA4132 2.776893e-03 1.944849e-02
Chlorobium 2.686638e-03 1.735463e-02
Butyribacter 2.665450e-03 2.625164e-02
Anaerorhabdus 2.588275e-03 9.581133e-03
Budvicia 2.586054e-03 9.218207e-03
Anaerotruncus 2.560824e-03 3.945328e-03
Dielma 2.369700e-03 3.784755e-03
Cetobacterium 2.216413e-03 6.456951e-03
Bilophila 2.076060e-03 3.433354e-03
HGM05232 1.944857e-03 3.177931e-03
JJ008 1.922642e-03 1.060181e-02
Gallalistipes 1.872220e-03 5.691823e-03
Methanothrix 1.861022e-03 1.802606e-02
Alistipes_A 1.829938e-03 3.396041e-03
Gallibacteroides 1.761646e-03 3.783251e-03
OLB14 1.748534e-03 7.893428e-03
CAKVBE01 1.683165e-03 5.685339e-03
GCA-2737665 1.607561e-03 1.047557e-02
RXIV01 1.594056e-03 1.515395e-02
Craterilacuibacter 1.478882e-03 1.128967e-02
FEN-1279 1.402641e-03 1.006339e-02
Chloroploca 1.400177e-03 1.355414e-02
Avirikenella 1.328205e-03 3.941073e-03
FEN-979 1.241677e-03 7.686017e-03
Intestinimonas 1.237653e-03 2.071632e-03
JADLHS01 1.230710e-03 7.499137e-03
Aureliella 1.154158e-03 9.332434e-03
Amedibacillus 1.048792e-03 3.272116e-03
Lamprocystis 1.048543e-03 4.898854e-03
Methylocystis 1.035186e-03 4.457229e-03
Novimethylophilus 9.868698e-04 5.353028e-03
CAJGBR01 9.829659e-04 1.426779e-03
UBA2475 9.743695e-04 6.097399e-03
Edwardsiella 9.489498e-04 3.070027e-03
RGIG5057 9.274101e-04 4.611188e-03
IGN3 9.217538e-04 8.213255e-03
Phocea 9.159914e-04 1.927484e-03
Romboutsia_D 8.946029e-04 1.950782e-03
UMGS1202 8.728213e-04 1.804112e-03
Romboutsia_A 8.584861e-04 5.034388e-03
UBA5066 8.403140e-04 5.601038e-03
UBA11358 8.313474e-04 4.169886e-03
CAIPUE01 8.191449e-04 2.427991e-03
Ferruginibacter 8.056303e-04 3.536915e-03
Anaerovorax 7.982578e-04 1.578540e-03
Azonexus 7.884278e-04 3.623383e-03
JABFSR01 7.691890e-04 3.989412e-03
JAGAJR01 7.650787e-04 1.550967e-03
Ruthenibacterium 7.410260e-04 2.767581e-03
UBA12294 7.405956e-04 3.885705e-03
OLB17 7.220263e-04 5.094091e-03
Bacteroides_G 7.161553e-04 3.813060e-03
JADKHC01 7.101304e-04 6.993974e-03
RGIG7389 6.985219e-04 1.404616e-03
Spyradomonas 6.922726e-04 2.236942e-03
Aminipila 6.825982e-04 9.886491e-04
UBA7488 6.802755e-04 2.335154e-03
Pseudoflavonifractor 6.421531e-04 1.658772e-03
Draconibacterium 6.410029e-04 2.707084e-03
Harryflintia 6.363666e-04 1.746416e-03
Evtepia 6.322927e-04 1.259868e-03
CAJATL01 6.317310e-04 4.568187e-03
Rhodoferax_C 6.305115e-04 4.874058e-03
RGIG5270 6.160249e-04 3.441629e-03
Methyloglobulus 5.812108e-04 2.705964e-03
UBA3961 5.724647e-04 2.628789e-03
Methanobacterium_A 5.711150e-04 3.871235e-03
Anaerotignum 5.595837e-04 1.290580e-03
Bacilliculturomica 5.428876e-04 1.259364e-03
Robinsoniella 5.385790e-04 2.056733e-03
14-2 5.263276e-04 2.565653e-03
OLB5 5.252756e-04 3.582377e-03
Hylemonella 5.252227e-04 5.172844e-03
Paludibacter 5.231717e-04 5.042377e-03
Scandinavium 5.102891e-04 3.105545e-03
JAERTD01 4.928572e-04 3.895817e-03
Shewanella 4.927823e-04 2.267869e-03
DYRC01 4.772738e-04 4.700602e-03
Copranaerobaculum 4.711817e-04 1.711813e-03
CAIPTY01 4.631029e-04 2.626182e-03
Eubacterium_R 4.598877e-04 4.529369e-03
WRKB01 4.365612e-04 8.420634e-04
JACRCG01 4.226413e-04 2.489191e-03
SKHV01 4.204799e-04 4.141246e-03
Egerieousia 4.156228e-04 1.178640e-03
JAGOBP01 4.086113e-04 3.836266e-03
Limnohabitans 4.058024e-04 2.403611e-03
RPPU01 4.053898e-04 3.992626e-03
JAKAJH01 3.996183e-04 2.723998e-03
Aliarcobacter 3.795084e-04 2.546493e-03
UBA5195 3.776642e-04 2.283696e-03
UBA6024 3.677665e-04 2.219403e-03
JAJBUQ01 3.634658e-04 7.678166e-04
UBA1306 3.564056e-04 3.510188e-03
AM-1111 3.542287e-04 2.303794e-03
Scatenecus 3.470350e-04 1.621431e-03
UBA1794 3.361116e-04 1.492346e-03
JAHHUI01 3.333468e-04 1.999495e-03
GWF2-50-10 3.327121e-04 2.480457e-03
CADEED01 3.265626e-04 2.177059e-03
CAZU01 3.230268e-04 1.502801e-03
JAGPHI01 3.061219e-04 1.510001e-03
UBA4417 2.893080e-04 2.849353e-03
TH-plancto1 2.891817e-04 2.848110e-03
JAAYQI01 2.884768e-04 1.172060e-03
CALXSC01 2.872357e-04 1.380046e-03
Methanocorpusculum 2.866192e-04 1.094065e-03
CAIQJJ01 2.816756e-04 2.774183e-03
Massiliimalia 2.770692e-04 1.158610e-03
CALURL01 2.735772e-04 1.381541e-03
Negativibacillus 2.673534e-04 8.605906e-04
CAIRTM01 2.647003e-04 1.610403e-03
JAEUNJ01 2.643866e-04 1.186509e-03
CAJLXD01 2.616752e-04 9.849718e-04
UBA2192 2.605813e-04 1.471595e-03
Coprobacillus 2.512556e-04 7.367047e-04
Plesiomonas 2.510777e-04 2.472828e-03
Leadbetterella 2.470890e-04 1.347542e-03
Lacibacter 2.466315e-04 2.198721e-03
JAAYKM01 2.396380e-04 2.360160e-03
UBA3254 2.373440e-04 1.827176e-03
WRDF01 2.355657e-04 7.059549e-04
RGDT01 2.328062e-04 2.292876e-03
JAHHTP01 2.321481e-04 7.443505e-04
JAFGIC01 2.320661e-04 2.285586e-03
M3007 2.317820e-04 1.292124e-03
Serratia_A 2.209635e-04 1.348450e-03
Holophaga 2.166536e-04 2.133790e-03
CAJAUT01 2.154250e-04 1.514456e-03
2-12-FULL-35-15 2.127537e-04 1.727718e-03
Methanoregula 2.115446e-04 1.818352e-03
CAIQQL01 2.012785e-04 1.796610e-03
Terracidiphilus 1.953616e-04 1.924089e-03
Syntrophorhabdus 1.890416e-04 1.546356e-03
Flavobacterium 1.829016e-04 1.620468e-03
UBA5026 1.821910e-04 1.348509e-03
Rahnella 1.803689e-04 1.253661e-03
SHXO01 1.797211e-04 8.927506e-04
CHH4-2 1.708571e-04 4.697032e-04
Morganella 1.661144e-04 1.371676e-03
Sulfuritalea 1.582309e-04 8.944958e-04
IOR16 1.569932e-04 3.560310e-04
Hespellia 1.564312e-04 8.181518e-04
M0103 1.549871e-04 1.052732e-03
MWCR01 1.541342e-04 1.081327e-03
JACRFF01 1.523242e-04 7.683019e-04
Avimicrobium 1.513856e-04 3.128958e-04
Rhodoferax 1.497042e-04 1.117247e-03
Aestuariivirga 1.447142e-04 5.908593e-04
PALSA-1004 1.297459e-04 9.992533e-04
Intestinibacillus 1.212242e-04 4.281023e-04
Aquisediminimonas 1.152657e-04 5.446202e-04
UBA668 1.119473e-04 7.628420e-04
Vitreimonas 1.094839e-04 6.706470e-04
Fluviibacter 1.058202e-04 3.751332e-04
JAGOMW01 1.026608e-04 7.766701e-04
PALSA-1444 9.517468e-05 4.833040e-04
Merdenecus 9.435047e-05 3.854333e-04
Massilioclostridium 9.062086e-05 2.962613e-04
Cardinium 9.033159e-05 5.611765e-04
UBA9973 8.917879e-05 8.783093e-04
Polynucleobacter 8.225897e-05 3.422233e-04
RGIG4140 8.096121e-05 5.359455e-04
UBA10108 7.929866e-05 7.810012e-04
JAGQMS01 7.555860e-05 3.616569e-04
Hepatoplasma 7.517161e-05 7.403545e-04
JAJQEJ01 7.487018e-05 2.711640e-04
Anaerobium 7.329179e-05 2.450951e-04
UBA8529 7.192224e-05 5.390355e-04
JAAYCI01 7.014809e-05 2.914153e-04
CAJBLF01 7.012992e-05 6.906996e-04
MGBC133411 6.940542e-05 4.023300e-04
JAEZVV01 6.890317e-05 6.000937e-04
UBA11704 6.344839e-05 5.321556e-04
RFTN01 6.279603e-05 3.586105e-04
JAFGVL01 6.033861e-05 5.942663e-04
Acinetobacter 5.992173e-05 4.649041e-04
RGIG8482 5.239573e-05 3.378165e-04
Methylopumilus_A 5.091526e-05 3.564476e-04
HGM16780 5.028810e-05 2.219329e-04
SSEF01 4.952088e-05 2.986606e-04
JAKJEI01 4.915817e-05 4.354164e-04
MGBC102946 4.876472e-05 4.802768e-04
Lumbricidophila 4.561574e-05 4.492630e-04
Brevinema 4.071840e-05 2.975509e-04
UBA8515 4.024405e-05 2.258398e-04
GWA2-36-10 2.884440e-05 2.345672e-04
JACRJP01 2.249398e-05 1.820714e-04
2-01-FULL-39-10-A 1.906267e-05 1.685139e-04
JAAZKV01 1.778707e-05 1.338011e-04
Aurantimicrobium 1.746277e-05 7.395454e-05
C7867-006 1.740558e-05 1.410053e-04
Cetobacterium_A 1.258077e-05 7.242913e-05
genus_arrange <- genus_summary %>%
    group_by(genus) %>%
    summarise(mean=sum(relabun)) %>%
    filter(genus != "g__")%>%
    arrange(-mean) %>%
    select(genus) %>%
    mutate(genus= sub("^g__", "", genus)) %>%
    pull()

#Per pond
genus_summary %>%
    left_join(sample_metadata,by=join_by(sample==sample)) %>%
    mutate(genus=factor(genus, levels=rev(genus_summary_sort %>% pull(genus)))) %>%
    filter(relabun > 0) %>%
    ggplot(aes(x=relabun, y=genus, group=genus, color=phylum)) +
        scale_color_manual(values=phylum_colors) +
        geom_jitter(alpha=0.5) + 
        facet_grid(.~region)+
        theme_minimal() + 
        labs(y="Family", x="Relative abundance", color="Phylum")